RCSB PDB - 8BBM: DNA binding domain of J-DNA Binding Protein 1 (JBP1)

 8BBM

DNA binding domain of J-DNA Binding Protein 1 (JBP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Distant sequence regions of JBP1 contribute to J-DNA binding.

de Vries, I.Ammerlaan, D.Heidebrecht, T.Celie, P.H.Geerke, D.P.Joosten, R.P.Perrakis, A.

(2023) Life Sci Alliance 6

  • DOI: https://doi.org/10.26508/lsa.202302150
  • Primary Citation of Related Structures:  
    8BBM

  • PubMed Abstract: 

    Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.


  • Organizational Affiliation

    Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymine dioxygenase JBP1170Leishmania tarentolaeMutation(s): 0 
Gene Names: JBP1
EC: 1.14.11.6
UniProt
Find proteins for Q9U6M1 (Leishmania tarentolae)
Explore Q9U6M1 
Go to UniProtKB:  Q9U6M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6M1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.286α = 90
b = 68.286β = 90
c = 185.842γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB-REDOrefinement
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands714.014.002

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary